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AAPM 2025 - 67th Annual Meeting & Exhibition of the American Association of Physicists in Medicine

AI Model Automatically Segments MRI Images

By MedImaging International staff writers
Posted on 20 Feb 2025

Image: Example MRI scans in the training dataset (Photo courtesy of Radiology, DOI:10.1148/radiol.241613)

Magnetic resonance imaging (MRI) plays a crucial role in providing detailed images of the human body, making it essential for diagnosing a wide range of medical conditions, from neurological disorders to musculoskeletal injuries. To interpret MRI images in depth, various anatomical structures such as organs, muscles, and bones are outlined or marked, a process known as segmentation. Traditionally, MRI images have been segmented manually, which is time-consuming, requires significant effort from radiologists, and is subject to variability between different readers. Automated systems offer the potential to reduce the radiologist's workload, minimize human errors, and deliver more consistent, reproducible results. Researchers have now developed and tested a robust artificial intelligence (AI) model capable of automatically segmenting major anatomical structures in MRI images, regardless of the sequence. In a study published in the journal Radiology, the AI model outperformed other publicly available tools.

Researchers at University Hospital Basel (Basel, Switzerland) developed an open-source automated segmentation tool called TotalSegmentator MRI, built on nnU-Net, a self-configuring framework that has set new benchmarks in medical image segmentation. This tool can adapt to new datasets with minimal user intervention, automatically adjusting its architecture, preprocessing, and training strategies to optimize performance. A similar model for CT (TotalSegmentator CT) is already in use by over 300,000 users worldwide, processing more than 100,000 CT images daily. In their retrospective study, the researchers trained TotalSegmentator MRI to provide sequence-independent segmentation of major anatomical structures using a randomly sampled dataset of 616 MRI and 527 CT exams.

The training set included segmentation data for 80 anatomical structures, which are commonly used for tasks such as measuring volume, characterizing diseases, planning surgeries, and conducting opportunistic screenings. To assess the model’s performance, Dice scores—metrics that measure the similarity between two sets of data—were calculated by comparing the predicted segmentations to the reference standards set by radiologists. The model performed well across all 80 structures, achieving a Dice score of 0.839 on an internal MRI test set. It significantly outperformed two publicly available segmentation models, with scores of 0.862, 0.838, and 0.560, respectively, and matched the performance of TotalSegmentator CT. Beyond research and AI product development, the researchers believe the model has the potential to be used clinically for treatment planning, monitoring disease progression, and conducting opportunistic screenings.

“We used a lot more data and segmented many more organs, bones and muscles than has been previously done. Our model also works across different MRI scanners and image acquisition settings,” said Jakob Wasserthal, Ph.D., Radiology Department research scientist at University Hospital Basel. “To our knowledge, our model is the only one that can automatically segment the highest number of structures on MRIs of any sequence. It’s a tool that helps improve radiologists’ work, makes measurements more precise and enables other measurements to be done that would have taken too much time to do manually.”

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80 (!!!!! 2155.065536499): SELECT show_live FROM jos_com_show_setting LIMIT 1

81 (53.167343139648): SELECT show_live FROM jos_com_show_setting LIMIT 1

82 (30.040740966797): SELECT show_live FROM jos_com_show_setting LIMIT 1

83 (25.98762512207): SELECT show_live FROM jos_com_show_setting LIMIT 1

84 (25.98762512207): SELECT show_live FROM jos_com_show_setting LIMIT 1

85 (26.941299438477): SELECT show_live FROM jos_com_show_setting LIMIT 1

86 (25.033950805664): SELECT show_live FROM jos_com_show_setting LIMIT 1

87 (25.98762512207): SELECT show_live FROM jos_com_show_setting LIMIT 1

88 (25.033950805664): SELECT show_live FROM jos_com_show_setting LIMIT 1

89 (25.033950805664): SELECT show_live FROM jos_com_show_setting LIMIT 1

90 (68.902969360352): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

91 (41.007995605469): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

92 (82.969665527344): SELECT dp.*, ch.title as channel, exp.name as author_name, exp.specialization as author_specialization, exp.images as author_photo FROM jos_deeppockets as dp LEFT JOIN jos_experts as exp ON exp.id = dp.author LEFT JOIN jos_deeppockets as ch ON dp.fid = ch.id WHERE 1=1 AND dp.cat=10 AND dp.id=294804092 AND (dp.type='deeppockets_item' OR dp.type='deeppockets_item_link') AND dp.published='1' LIMIT 1

93 (79.870223999023): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

94 (41.961669921875): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

95 (398.15902709961): SELECT dp.*, ch.title as channel, exp.name as author_name, exp.specialization as author_specialization, exp.images as author_photo FROM jos_deeppockets as dp LEFT JOIN jos_experts as exp ON exp.id = dp.author LEFT JOIN jos_deeppockets as ch ON dp.fid = ch.id WHERE 1=1 AND dp.id=294804092 AND (dp.type='deeppockets_item' OR dp.type='deeppockets_item_link') AND dp.published='1' LIMIT 1

96 (567.91305541992): SELECT dp.name, dp.id, dp2.name as channel, ex.name as author_name, ex.specialization, ex.images FROM jos_deeppockets as dp LEFT JOIN jos_experts as ex ON ex.id = dp.author LEFT JOIN jos_deeppockets as dp2 ON dp2.id = dp.fid WHERE dp.author != 0 AND dp.cat = 10 AND dp.published = 1 AND ( (dp.fid = 294743300) OR (dp.fid = 294743301) OR (dp.fid = 294743302) OR (dp.fid = 294743303) OR (dp.fid = 294743304) OR (dp.fid = 294743305) OR (dp.fid = 294743306) OR (dp.fid = 294743307) OR (dp.fid = 294743308) OR (dp.fid = 294743309) OR (dp.fid = 294743310) ) ORDER BY RAND() LIMIT 1

97 (452.99530029297): SELECT dp.name, dp.id, dp2.name as channel, ex.name as author_name, ex.specialization, ex.images FROM jos_deeppockets as dp LEFT JOIN jos_experts as ex ON ex.id = dp.author LEFT JOIN jos_deeppockets as dp2 ON dp2.id = dp.fid WHERE dp.author != 0 AND dp.cat = 10 AND dp.published = 1 AND ( (dp.fid = 294743300) OR (dp.fid = 294743301) OR (dp.fid = 294743302) OR (dp.fid = 294743303) OR (dp.fid = 294743304) OR (dp.fid = 294743305) OR (dp.fid = 294743306) OR (dp.fid = 294743307) OR (dp.fid = 294743308) OR (dp.fid = 294743309) OR (dp.fid = 294743310) ) ORDER BY RAND() LIMIT 1

98 (80.108642578125): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

99 (58.889389038086): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

100 (72.002410888672): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

101 (88.214874267578): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

102 (65.088272094727): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

103 (38.862228393555): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

104 (57.93571472168): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

105 (36.954879760742): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

106 (392.91381835938): SELECT * FROM trending_articles WHERE `journal_id` = 10 AND `timestamp` <= NOW() + INTERVAL 7 DAY ORDER BY `order`

107 (!!!!! 20771.980285645): SELECT * FROM jos_deeppockets WHERE jos_deeppockets.cat = 10 AND jos_deeppockets.type = 'deeppockets_item' AND jos_deeppockets.published = 1 AND jos_deeppockets.created + INTERVAL 14 DAY >= NOW() ORDER BY jos_deeppockets.hits DESC LIMIT 7

108 (441.7896270752): SELECT fid FROM jos_deeppockets WHERE cat=10 AND id=294804092 AND type='deeppockets_item' AND published='1' union SELECT fid FROM jos_deeppockets_archive WHERE cat=10 AND id=294804092 AND type='deeppockets_item' AND published='1' LIMIT 1

109 (82.969665527344): ( SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.video != '' AND dp.video_source != '' AND dp.cat = 10 AND dp.published = 1 AND dp.type != 'deeppockets_item_link' ORDER BY created DESC LIMIT 3 ) UNION ( SELECT dpa.id, dpa.name, dpa.title, dpa.video, dpa.video_source, dpa.created FROM jos_deeppockets_archive AS dpa WHERE dpa.video != '' AND dpa.video_source != '' AND dpa.cat = 10 AND dpa.published = 1 AND dpa.type != 'deeppockets_item_link' ORDER BY created DESC LIMIT 3 ) ORDER BY created DESC LIMIT 3

110 (34.809112548828): ( SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.video != '' AND dp.video_source != '' AND dp.cat = 10 AND dp.published = 1 AND dp.type != 'deeppockets_item_link' ORDER BY created DESC LIMIT 3 ) UNION ( SELECT dpa.id, dpa.name, dpa.title, dpa.video, dpa.video_source, dpa.created FROM jos_deeppockets_archive AS dpa WHERE dpa.video != '' AND dpa.video_source != '' AND dpa.cat = 10 AND dpa.published = 1 AND dpa.type != 'deeppockets_item_link' ORDER BY created DESC LIMIT 3 ) ORDER BY created DESC LIMIT 3

111 (33.855438232422): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294803337 LIMIT 1

112 (27.894973754883): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294803337 LIMIT 1

113 (33.855438232422): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294803276 LIMIT 1

114 (28.848648071289): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294803276 LIMIT 1

115 (28.133392333984): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets_archive AS dp WHERE dp.id = 294803276 LIMIT 1

116 (28.133392333984): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets_archive AS dp WHERE dp.id = 294803276 LIMIT 1

117 (28.133392333984): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294802958 LIMIT 1

118 (30.040740966797): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294802958 LIMIT 1

119 (422.00088500977): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

120 (178.09867858887): SELECT name FROM jos_deeppockets WHERE id=212

121 (33.140182495117): SELECT name FROM jos_deeppockets WHERE id=212

122 (864.98260498047): SELECT *, DATE_FORMAT(publish_up,'%d %b %Y') AS date_publish_up, DATE_FORMAT(publish_down,'%d %b %Y') AS date_publish_down FROM jos_events WHERE state=1 AND publish_up > NOW() and extra_info REGEXP '((;)|(^))212((;)|($))' AND catid IN (0,110) ORDER BY publish_up ASC LIMIT 3

123 (544.78645324707): SELECT *, DATE_FORMAT(publish_up,'%d %b %Y') AS date_publish_up, DATE_FORMAT(publish_down,'%d %b %Y') AS date_publish_down FROM jos_events WHERE state=1 AND publish_up > NOW() and extra_info REGEXP '((;)|(^))212((;)|($))' AND catid IN (0,110) ORDER BY publish_up ASC LIMIT 3

124 (75.101852416992): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

125 (47.922134399414): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

126 (!!!!! 7839.9181365967): TRUNCATE TABLE jos_trademed_module

127 (94.890594482422): SELECT dp.*, ch.title as channel, exp.name as author_name, exp.specialization as author_specialization, exp.images as author_photo FROM jos_deeppockets as dp LEFT JOIN jos_experts as exp ON exp.id = dp.author LEFT JOIN jos_deeppockets as ch ON dp.fid = ch.id WHERE 1=1 AND dp.cat=10 AND dp.id=294804092 AND (dp.type='deeppockets_item' OR dp.type='deeppockets_item_link') AND dp.published='1' LIMIT 1

128 (858.06846618652): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

129 (60.796737670898): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

130 (92.029571533203): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

131 (56.982040405273): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

132 (!!!!! 1173.0194091797): SELECT jos_item.* FROM jos_item INNER JOIN jos_number ON jos_item.numberID=jos_number.id WHERE 1=1 AND (jos_item.imgMini<>'') AND jos_item.type='L' AND jos_item.numberID= ( SELECT jos_number.id FROM jos_number WHERE jos_number.journalID IN (10) and jos_number.id in (select distinct jos_number.id from jos_number join jos_item on jos_item.numberid=jos_number.id where jos_item.type='P') ORDER BY (CONVERT(SUBSTRING(issue,1,2),SIGNED) + (CONVERT(SUBSTRING(issue,3,2),SIGNED)*100)) DESC LIMIT 0,1 ) ORDER BY RAND() DESC LIMIT 6

133 (49.114227294922): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

134 (38.862228393555): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

135 (77.009201049805): SELECT fid FROM jos_deeppockets WHERE cat=10 AND id=294804092 AND type='deeppockets_item' AND published='1' union SELECT fid FROM jos_deeppockets_archive WHERE cat=10 AND id=294804092 AND type='deeppockets_item' AND published='1' LIMIT 1

136 (30.994415283203): select distinct links.* from jos_textlinks links join jos_textlinks_placement placement on links.id=placement.link_id where journal_id=(10) and (channel_id=212 or channel_id is null)

137 (31.948089599609): select distinct links.* from jos_textlinks links join jos_textlinks_placement placement on links.id=placement.link_id where journal_id=(10) and (channel_id=212 or channel_id is null)

138 (35.04753112793): SELECT livesite FROM jos_dp_categories WHERE id=10 AND published='1' LIMIT 1

139 (57.93571472168): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

140 (41.007995605469): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294804092 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294804092 AND published='1' LIMIT 1

141 (37.908554077148): select jos_twitters.link from jos_twitters where cat=10

142 (30.994415283203): select jos_facebook.link from jos_facebook where cat=10

143 (30.994415283203): select jos_google_plus.link from jos_google_plus where cat=10

144 (30.994415283203): select jos_linkedin.link from jos_linkedin where cat=10

145 (226.97448730469): update jos_bannersmanager_banner set impmade=impmade+1 where id in(14615,14202,14203)

146 (!!!!! 1065.0157928467): insert into jos_banners_delta values (14615,'2025-06-21 02:21:50','216.73.216.120','view'),(14202,'2025-06-21 02:21:50','216.73.216.120','view'),(14203,'2025-06-21 02:21:50','216.73.216.120','view')

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